def createMorphoMlFile(fileName, cell): ''' Convert to new neuroml structures and write ''' if not muscle_dict.has_key(cell.name): neuroMlwriter = NeuroMlWriter(fileName, cell.name) neuroMlwriter.addCell(cell) neuroMlwriter.writeDocumentToFile() return # # Incomplete code to use the neuroml interface to write the file, # used for muscles, doesn't produce good enough result on neurons yet. # seg0 = cell.segments[0].position soma = Segment(proximal=cvt_pt(seg0.proximal_point), distal=cvt_pt(seg0.distal_point)) soma.name = 'Soma' soma.id = 0 axon_segments = [] for seg1 in cell.segments[1:]: parent = SegmentParent(segments=seg1.parent) if seg1.position.proximal_point is None: p = None else: p = cvt_pt(seg1.position.proximal_point) axon_segment = Segment(proximal = p, distal = cvt_pt(seg1.position.distal_point), parent = parent) axon_segment.id = seg1.id axon_segment.name = seg1.name axon_segments.append(axon_segment) morphology = Morphology() morphology.segments.append(soma) morphology.segments += axon_segments morphology.id = 'morphology_' + cell.name nml_cell = neuroml_Cell() nml_cell.id = cell.name nml_cell.morphology = morphology doc = NeuroMLDocument() doc.cells.append(nml_cell) #addCell(doc, cell) doc.id = "TestNeuroMLDocument" writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)
def createMorphoMlFile(fileName, cell): ''' Convert to new neuroml structures and write ''' if not muscle_dict.has_key(cell.name): neuroMlwriter = NeuroMlWriter(fileName, cell.name) neuroMlwriter.addCell(cell) neuroMlwriter.writeDocumentToFile() return # # Incomplete code to use the neuroml interface to write the file, # used for muscles, doesn't produce good enough result on neurons yet. # seg0 = cell.segments[0].position soma = Segment(proximal=cvt_pt(seg0.proximal_point), distal=cvt_pt(seg0.distal_point)) soma.name = 'Soma' soma.id = 0 axon_segments = [] for seg1 in cell.segments[1:]: parent = SegmentParent(segments=seg1.parent) if seg1.position.proximal_point is None: p = None else: p = cvt_pt(seg1.position.proximal_point) axon_segment = Segment(proximal=p, distal=cvt_pt(seg1.position.distal_point), parent=parent) axon_segment.id = seg1.id axon_segment.name = seg1.name axon_segments.append(axon_segment) morphology = Morphology() morphology.segments.append(soma) morphology.segments += axon_segments morphology.id = 'morphology_' + cell.name nml_cell = neuroml_Cell() nml_cell.id = cell.name nml_cell.morphology = morphology doc = NeuroMLDocument() doc.cells.append(nml_cell) #addCell(doc, cell) doc.id = "TestNeuroMLDocument" writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)
def createMorphoMlFile(fileName, cell): ''' Convert to new neuroml structures and write ''' seg0 = cell.segments[0].position soma = Segment(proximal=cvt_pt(seg0.proximal_point), distal=cvt_pt(seg0.distal_point)) soma.name = 'Soma' soma.id = 0 axon_segments = [] for seg1 in cell.segments[1:]: parent = SegmentParent(segments=seg1.parent) if seg1.position.distal_point is None: p = None else: p = cvt_pt(seg1.position.distal_point) axon_segment = Segment(proximal=p, distal=cvt_pt(seg1.position.distal_point), parent=parent) axon_segment.id = seg1.id axon_segment.name = seg1.name axon_segments.append(axon_segment) morphology = Morphology() morphology.segments.append(soma) morphology.segments += axon_segments morphology.id = 'morphology_' + cell.name nml_cell = neuroml_Cell() nml_cell.id = cell.name nml_cell.morphology = morphology doc = NeuroMLDocument() #doc.name = "Test neuroML document" doc.cells.append(nml_cell) doc.id = fileName writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)
def createMorphoMlFile(fileName, cell): ''' Convert to new neuroml structures and write ''' seg0 = cell.segments[0].position soma = Segment(proximal=cvt_pt(seg0.proximal_point), distal=cvt_pt(seg0.distal_point)) soma.name = 'Soma' soma.id = 0 axon_segments = [] for seg1 in cell.segments[1:]: parent = SegmentParent(segments=seg1.parent) if seg1.position.distal_point is None: p = None else: p = cvt_pt(seg1.position.distal_point) axon_segment = Segment(proximal = p, distal = cvt_pt(seg1.position.distal_point), parent = parent) axon_segment.id = seg1.id axon_segment.name = seg1.name axon_segments.append(axon_segment) morphology = Morphology() morphology.segments.append(soma) morphology.segments += axon_segments morphology.id = 'morphology_' + cell.name nml_cell = neuroml_Cell() nml_cell.id = cell.name nml_cell.morphology = morphology doc = NeuroMLDocument() #doc.name = "Test neuroML document" doc.cells.append(nml_cell) doc.id = fileName writers.NeuroMLWriter.write(doc, "Output/%s.nml" % fileName)
def neuroml_network(cells, response): """ Write a list of Cell instances. cells: a list of Cell instances. response: somewhere to write to, like an HttpResponse Returns nothing. """ doc = NeuroMLDocument() doc.cells.extend(cells) doc.id = "NeuroMLDocument" namespacedef = 'xmlns="http://www.neuroml.org/schema/neuroml2"' \ + ' xmlns:xi="http://www.w3.org/2001/XInclude"' \ + ' xmlns:xs="http://www.w3.org/2001/XMLSchema"' \ + ' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"' \ + ' xsi:schemaLocation="http://www.w3.org/2001/XMLSchema"' doc.export( response, 0, name_="neuroml", namespacedef_=namespacedef) return response
def neuroml_network(cells, response): """ Write a list of Cell instances. cells: a list of Cell instances. response: somewhere to write to, like an HttpResponse Returns nothing. """ doc = NeuroMLDocument() doc.cells.extend(cells) doc.id = "NeuroMLDocument" namespacedef = 'xmlns="http://www.neuroml.org/schema/neuroml2"' \ + ' xmlns:xi="http://www.w3.org/2001/XInclude"' \ + ' xmlns:xs="http://www.w3.org/2001/XMLSchema"' \ + ' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"' \ + ' xsi:schemaLocation="http://www.w3.org/2001/XMLSchema"' doc.export(response, 0, name_="neuroml", namespacedef_=namespacedef) return response